Numerous non-genetic variables interact with gene variants to influence alcohol use, dependence, and relapse. One key influence is a complex mix of stressors. In common with other components of this INIA application, this project explores genetic, molecular, and cellular substrates of alcohol consumption in response to stress. Our focus is on using new high-resolution gene mapping resources and methods to dissect genetic interactions between alcohol, stress, and forebrain-midbrain anatomy. We use well characterized behavioral paradigm that are combined for the first time with sophisticated stereology and immunohistochemical analysis of the amygdala and key neuromodulatory inputs to the forebrain. Data from the molecular and structural analyses will be combined with EtOH-stress interaction measures to define shared and unique genetic determinants. The first aim is to systematically apply new quantitative trait locus (QTL) mapping methods to fine map alcohol and stress-related genes in mice. More than ten loci are being mapped and remapped with high precision (a critical region of 1-2 cM) using a set of -100 new types of recombinant inbred (RI) strains, an novel RI intercross (RIX) method, and interval-specific congenic lines. In parallel with these genetic studies, we will explore genetic and epigenetic interactions and codeterrninants of stress and alcohol consumption. We intend to systematically map genes that influence the number and distribution of three major neurotransmitter systems that modulate basal forebrain physiology serotoninergic cells in the dorsal raphe, noradrenergic neurons in the locus coeruleus, and dopaminergic cells in the midbrain. This aim links our analysis closely to the other transmitter-related components of the INIA. We will use unbiased stereological methods. We anticipate that the synergy between the structural and functional analysis will allow us to far more efficiently generate candidate genes that influence the development of alcoholism in humans.